I am not saying that a Harlequin could beat a Primarch in a fight. I am saying that if a Harlequin were to get a lucky punch on a Primarch, the weapon would kill the Primarch.
Given that Fulgrim survived a sniper's bullet to the brain pan i'm not so sure that's true.Seeing as how that would not work with at least one primarch, I'd say that is a gross assumption. We don't know who else could be a perpetual or something crazy. The primarchs genetic abilities are a mystery. Fulgrim killed an Avatar which could destroy a lot of Harlequins. The Avatars are the equivalent of a primarch level characters. You're also assuming the biology of a primarch could not heal instantly from internal damage. The only thing we've seen defeat their biology has been warp poison (Horus and Gulliman) and a decapitation (Ferrus Manus and Kurze). Now this weapons seems dangerous but getting through primarch armor, speed, and skill will be dangerous. I don't see a Harlequin getting this done to be real with you. It's the same argument of the Nemesis novel with the Execution force. A Vindicate could kill a primarch, if he got the shot. How likely is that?